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- PDB-4p10: pro-carboxypeptidase U In Complex With 5-(3-aminopropyl)-1-propyl... -

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Basic information

Entry
Database: PDB / ID: 4p10
Titlepro-carboxypeptidase U In Complex With 5-(3-aminopropyl)-1-propyl-6,7-dihydro-4H-benzimidazole-5-carboxylic acid
ComponentsCarboxypeptidase B2
KeywordsHYDROLASE / inhibitor / drug discovery
Function / homology
Function and homology information


carboxypeptidase U / positive regulation of extracellular matrix constituent secretion / negative regulation of hepatocyte proliferation / negative regulation of plasminogen activation / metallocarboxypeptidase activity / Metabolism of Angiotensinogen to Angiotensins / negative regulation of fibrinolysis / fibrinolysis / Regulation of Complement cascade / liver regeneration ...carboxypeptidase U / positive regulation of extracellular matrix constituent secretion / negative regulation of hepatocyte proliferation / negative regulation of plasminogen activation / metallocarboxypeptidase activity / Metabolism of Angiotensinogen to Angiotensins / negative regulation of fibrinolysis / fibrinolysis / Regulation of Complement cascade / liver regeneration / cellular response to glucose stimulus / protein catabolic process / blood coagulation / response to xenobiotic stimulus / proteolysis / extracellular space / extracellular exosome / zinc ion binding / extracellular region
Similarity search - Function
Carboxypeptidase B2 / Metallocarboxypeptidase-like / Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide / Carboxypeptidase activation peptide / Peptidase family M14 domain profile. / Zn_pept / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase / Zn peptidases ...Carboxypeptidase B2 / Metallocarboxypeptidase-like / Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide / Carboxypeptidase activation peptide / Peptidase family M14 domain profile. / Zn_pept / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-2B8 / Carboxypeptidase B2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHallberg, K. / Sjogren, T.
CitationJournal: Bioorg.Med.Chem. / Year: 2014
Title: Design and synthesis of conformationally restricted inhibitors of active thrombin activatable fibrinolysis inhibitor (TAFIa).
Authors: Brink, M. / Dahlen, A. / Olsson, T. / Polla, M. / Svensson, T.
History
DepositionFeb 21, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_radiation_wavelength ...chem_comp / diffrn_radiation_wavelength / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carboxypeptidase B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0095
Polymers46,3791
Non-polymers6304
Water2,846158
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint7 kcal/mol
Surface area16160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.576, 49.243, 95.048
Angle α, β, γ (deg.)90.00, 93.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Carboxypeptidase B2 / / Carboxypeptidase U / CPU / Plasma carboxypeptidase B / pCPB / Thrombin-activable fibrinolysis inhibitor / TAFI


Mass: 46379.387 Da / Num. of mol.: 1 / Mutation: H355Y, H357Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CPB2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96IY4, carboxypeptidase U
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 161 molecules

#2: Chemical ChemComp-2B8 / (5R)-5-(3-aminopropyl)-1-propyl-4,5,6,7-tetrahydro-1H-benzimidazole-5-carboxylic acid


Mass: 265.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H23N3O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Crystallisation was done using the hanging drop method equilibrating over a well solution containing 10% (w/v) PEG20k, 2% dioxane and 0.1M bicine pH 9.0. Crystals were then soaked in well ...Details: Crystallisation was done using the hanging drop method equilibrating over a well solution containing 10% (w/v) PEG20k, 2% dioxane and 0.1M bicine pH 9.0. Crystals were then soaked in well solution supplemented with 1 mM compound

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Jan 28, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 30908 / % possible obs: 99.1 % / Redundancy: 4.1 % / Net I/σ(I): 7.1
Reflection shellResolution: 2→2.05 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 2.7 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZG7

1zg7


Resolution: 2→94.91 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.016 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21812 1547 5 %RANDOM
Rwork0.18398 ---
obs0.18572 29202 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.115 Å2
Baniso -1Baniso -2Baniso -3
1--1.66 Å2-0 Å20.51 Å2
2--3.79 Å2-0 Å2
3----2.17 Å2
Refinement stepCycle: 1 / Resolution: 2→94.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3254 0 38 158 3450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193383
X-RAY DIFFRACTIONr_bond_other_d0.0010.023115
X-RAY DIFFRACTIONr_angle_refined_deg1.7411.9434601
X-RAY DIFFRACTIONr_angle_other_deg0.9237151
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4195401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.9223.585159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16815552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5831519
X-RAY DIFFRACTIONr_chiral_restr0.1190.2498
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023812
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02823
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1332.5561607
X-RAY DIFFRACTIONr_mcbond_other2.1312.5551606
X-RAY DIFFRACTIONr_mcangle_it2.9253.8252007
X-RAY DIFFRACTIONr_mcangle_other2.9243.8272008
X-RAY DIFFRACTIONr_scbond_it2.6772.7941776
X-RAY DIFFRACTIONr_scbond_other2.6772.7941776
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.794.0992595
X-RAY DIFFRACTIONr_long_range_B_refined4.92721.0314074
X-RAY DIFFRACTIONr_long_range_B_other4.86520.954033
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.003→2.055 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 111 -
Rwork0.235 2129 -
obs--97.52 %

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